Off the coast of Panama, a team of archaeologists uncovers a ship that may have belonged to one of the most famous pirates who ever lived.

I wrap my hands around the straight iron blade. It's probably a 17th-century rapier, I'm told, but it'd hard to know for sure. The handle is missing, and though I can see and feel its fuller groove, a layer of sea shells and some sort of hardened concretion cover the blade's finer details. "That's either calcium carbonate or coralline," Texas State University archaeologist Fritz Hanselmann tells me as he takes the blade and places it in a makeshift holder his crew had just MacGyvered from a metal CD rack, rebar, and scraps of a yoga mat.

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We're standing on the deck of a 90-foot yacht floating at the mouth of Panama's Chagres River, where it flows into the Caribbean Sea. It's early July, and the choppy water is a murky shade of green that makes it impossible to see more than a few feet into its depth. A shame, since a centuries-old shipwreck lies only 20 or so feet below us, and clearer conditions might have let us see it from the surface.

This boat's crew of archaeologists and divers, led by Hanselmann and including volunteers from the National Park Service's Submerged Resources Center and the NOAA/UNC-Wilmington Aquarius Reef Base, has spent the past several years tracking and excavating the contents of the wreck. Today's bounty is relatively modest: the sword and a series of lead seals likely used for imprinting wax. But the ship holds greater treasures that are still to be retrieved: more than 80 chests and barrels whose contents have the potential to confirm whether the ship below us once belonged to one of the most famous pirates who ever lived.

On December, 18, 1670, Welsh privateer Captain Henry Morgan and a crew of roughly 1500 cutthroats, plunderers, and buccaneers set sail from notorious pirate stronghold Port Royal, Jamaica. Their mission: to sack Panama City, a stopping point for ships seeking to transport gold and silver mined in Peru back to Europe, which made it the wealthiest city in New Spain.

This was no slipshod pirate's plan—Morgan was known as one of the great military leaders of his time. Before Panama City, Morgan had sent a brigade of three ships and nearly 500 men to destroy Fort San Lorenzo, a cliffside fortress that guarded the mouth of the Chagres and protected the city. After a bloody battle, Morgan's men succeeded. With Fort San Lorenzo conquered, there was little to keep his entire fleet of 36 ships from raiding nearby Panama City.

The pirates conquered the city and occupied it for nearly a month. But as Morgan entered the mouth of the river on his way to victory, five of his ships sunk—not from battle, but from the razor-sharp reef that lay as little as a foot beneath the surface. To this day, the wreckage of these ships has remained on the ocean floor.

In September 2010, Hanselmann's team recovered six iron cannons from the area of the Chagres River where Morgan's ships were known to have gone down. Those cannons meant that ships and the rest of their treasures were probably nearby, but Hanselmann lacked the funds to survey and excavate the surrounding area.

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This is where the rum comes in.

Anyone who isn't a scholar of 17th-century naval history probably knows Captain Morgan more as a spiced rum spokesman than a real historical pirate. It's not surprising, then, that the rum company would see an increased awareness of all things Morgan could be a win for the brand, and decided to kick in some funding for the expedition.

"We're always striving to learn more about the history of our brand icon," says Tom Herbst, brand director at Captain Morgan USA. "We think the artifacts uncovered during these missions will help bring Henry Morgan and his adventures to life."

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With rum money fueling his expedition, Hanselmann set out to find Morgan's wrecks and cultural artifacts and get them to the Patronato Panama Viejo, a nongovernmental group in Panama that works with the National Institute of Culture to preserve the ruins of the original Panama City.

"Protecting underwater heritage from looters and others who would sell artifacts is one part of why we do what we do," Hanselmann says. "One major reason for preservation of artifacts is making our discovery available to the general public, and any artifact that is recovered through archaeological methods needs to be conserved so that it does not decompose or fall apart."

At its heart, underwater archaeology is a two-step process: Scan and dig.

If you want to find something hidden underwater, first you must find the anomalies in your search area—inconsistencies in the seafloor that could turn out to be a ship, a cannon, or a chest. Well-equipped archaeologists typically scan the floor using either sonar or magnetometers. When it comes to the digging, recovery diving is all about the process of elimination. Once you have your target points, you strap on your scuba suit and dig them up, one at a time, until you find what you're looking for.

Hanselmann's shipwreck search began with magnetometers. These tools look like small torpedoes and detect deviations in the earth's magnetic field caused by iron objects. Shipwreck hunters typically tow the magnetometers behind boats in parallel lines as they canvas a target area (imagine a lawnmower covering an entire lawn.)

Unlike sonar, magnetometer scans don't produce a picture of the seafloor. "Instead, they produce a position and a gamma value which reflects the earth's magnetic field, measured in gammas or nanoteslas, for that specific point," says Bert Ho from the National Park Service Submerged Resources Center, the lead survey archaeologist on the Morgan project. "Once we have this data we can create contours... From these contours we can produce points we refer to as magnetic anomalies, and these are where we investigate visually by diving."

Hanselmann's crew used two different magnetometers loaned by the Submerged Resources Center. (Gear geeks: One was a Geometrics G-882 cesium vapor model, and the other a Marine Magentics Explorer model that featured an Overhauser sensor.) Together they found more than 100 anomalies, one of which turned out to be the ship. "We found what looked to be like some coral-encrusted wood, which is what led us to conduct a test excavation there," Hanselmann says.

Depending on the specific portion, the wreck sat anywhere from few inches to more than 3 feet under the mud. The crew then used a combination of dredge and water jet to excavate the ship from the sand-and-silt seafloor. After uncovering a good portion of the wreck, Hanselmann's crew drew a map of it using surprisingly old-fashioned tools—tape measures and underwater slates.

"The map of the shipwreck comes from physically taking measurements of the various features of the site over several series of dives," Hanselmann says. "We lay a baseline and measure artifacts and parts and pieces of the ship from the baseline. We then return to land and create a scaled map of the site." The team then divides the map into sectors and searches the sectors one at a time.

In the weeks since my visit to the dive site, Hanselmann's team has pulled a single chest and a single barrel up to the surface. Centuries of saltwater and sediment have worn them down into rough, rocklike shapes, but they may yet be able to tell the archaeologists whether this was in fact Morgan's ship.

Of course, Hanselmann's crew would love to crack them open and see what's inside. But sudden exposure to air could ruin their contents. First, the objects have to go through a months-long preservation process that includes electrolysis-driven salt removal and an endless series of baths. Only then can the team view the contents and find out whether they have anything to do with Captain Henry Morgan.

Hanelmann seems optimistic but increasingly prepared for the possibility that this ship was not one of Morgan's. The chief hole he sees in his own hope: With more than 80 chests, there may be just too many goodies onboard. "I compare it to a visit to a grocery store—you wouldn't show up with a full trunk," Hanselmann says. "If you're going to plunder Panama City, it doesn't make sense to show up with a full ship."

More likely, according to Hanselmann, is that the wreck was a Spanish merchant ship. Even so, he doesn't seem too upset. The vessel is loaded to the gills with important artifacts, and Morgan's actual boats can't be too far off.